Posts Tagged ‘wikipedia’

In Support of Wikipedia

January 17, 2012

Many of you will be aware of the proposed web blackout in response to the Stop Online Piracy Act which is currently going through the U.S. House of Representatives (you can read the BBC’s explanation of the Act here). If this Act is enforced, it has far-reaching consequences for the overall freedom of the internet. Editors of the English Wikipedia have taken the decision to close the English Wikipedia for 24 hours, starting at 0500 hrs on Wednesday 18th January. To respect this protest, we will also be making our Wikipedia content unavailable during this time.

You’ll still be able to access all the non-Wikipedia content – that is, all the covariance models and HMMs describing families, domain graphics, full and seed alignments, as well as our species trees.

Posted by Sarah and Alex

No, seriously, we’ve made a release

April 1, 2011

Well, it should have been out about 6 months ago, but finally the long awaited Pfam release 25.0 is here! Release 25.0 contains a total of 12273 families, with 384 new families and 21 families killed since the latest release.  Pfam 25.0 is based on UniProt release 2010_05. Those of you who follow Pfam closely will be familiar with the fact the sequence coverage (the number of sequences in Pfamseq containing at least one Pfam match) has hovered at or just below 75%.  Despite the addition of only a modest number of new families in this release, the sequence coverage is now 76.69% of all proteins in Pfamseq contain a match to at least one Pfam domain.  53.86% of all residues in the sequence database fall within Pfam domains.

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The Rfam NAR paper is out!

December 9, 2010

This is a belated announcement of the release of the latest Rfam database article in the NAR database issue:
[1] Gardner PP, Daub J, Tate J, Moore BL, Osuch IH, Griffiths-Jones S, Finn RD, Nawrocki EP, Kolbe DL, Eddy SR, Bateman A. (2010) Rfam: Wikipedia, clans and the “decimal” release. Nucleic Acids Res.

In this publication we discuss the success of the relationship between Wikipedia and Rfam. This includes a fun analysis of the degree of vandalism the RNA pages have received with respect to the number of useful edits. We also discuss the new clans that explicitly link families that share an evolutionary relationship yet are too divergent to be sensibly aligned, the latest “decimal” release and our future plans.

While you are there, check out the latest miRBase paper and the new miRBase blog:
[2] Kozomara A, Griffiths-Jones S. (2010) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res.

Our friends over at the EBI have 2 papers describing the all-important nucleotide sequence archives:
[3] Cochrane G, Karsch-Mizrachi I, Nakamura Y; On behalf of the International Nucleotide Sequence Database Collaboration. (2010) The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res.

[4] Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-Tárraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, Hoad G, Jang M, Pakseresht N, Plaister S, Radhakrishnan R, Reddy K, Sobhany S, Ten Hoopen P, Vaughan R, Zalunin V, Cochrane G. (2010) The European Nucleotide Archive. Nucleic Acids Res.

The ENSEMBL series of genome databases has had an update:
[5] Flicek P et al. (2010) Ensembl 2011. Nucleic Acids Res.

Also, see the very useful nomenclature efforts of the “(Human Genome Organisation) Gene Nomenclature Committee”:
[6] Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA. (2010) genenames.org: the HGNC resources in 2011. Nucleic Acids Res.

Plans for Rfam 2010-2011

June 30, 2010

Besides running RNA informatics courses Rfam peoples will be working on the usual summer family-building exercise together with a bright summer student. Priority number one will be building the published RNA Biology articles that we ran out of time to do for the Rfam 10.0 release:

SmY MRP Yfr2 tmRNA
Trypanosomal H/ACA ncRNAs GIR1 U3 SRP
influenza pseudoknot ptaRNA1 RsaOG rsmX

An exciting trend we’re starting to see is groups appending machine parsable alignments to their papers and writing Wikipedia articles for their families outside of the RNA families track. Of particular note are the 81 families from Zasha Weinberg’s latest papers [1-3] (see the table below). Also, Daniel Gautheret’s and Wade Winkler’s groups are supporting this effort with their respective CsfG RNA [4] and EAR motif [5] articles. Rightly or wrongly we are crediting some of this to the increased exposure of Rfam’s requirements from the RNA families track at the journal RNA Biology. This, by the way, for the first time has an impact factor, which is a fantastic 5.559. RNA Biology is punching well above its weight for now, long may this continue. Once our super summer student has finished with these (much easier families) he’ll be moving on to our terrifyingly long list of potential Rfam families that are waiting to be built. If you see anything on this list you might be interested in writing an RNA biology article for then please let us know as soon as possible.

In other news, we’re still hunting for good people to join a revamped Xfam group. In a few days we’ll be advertising Curator positions and we’re still looking for a Senior Computational Biologist. Check the Sanger Jobs site over the next few days.

[1] Weinberg Z, Wang JX, Bogue J, Yang J, Corbino K, Moy RH, Breaker RR (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biology

[2] Weinberg Z, Perreault J, Meyer MM, Breaker RR (2009) Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis. Nature.

[3] Meyer MM, Ames TD, Smith DP, Weinberg Z, Schwalbach MS, Giovannoni SJ, Breaker RR. (2009) Identification of candidate structured RNAs in the marine organism ‘Candidatus Pelagibacter ubique’. BMC Genomics.

[4] Marchais A, Duperrier S, Gautheret D, Stragier P. (2010). A sporulation-specific, small noncoding RNA highly conserved in endospore formers. In preparation.

[5]  Irnov I & Winkler WC (2010) A regulatory RNA required for antitermination of biofilm and capsular polysaccharide operons in Bacillales. Mol Microbiol.

6S-Flavo Acido-1 Acido-Lenti-1 Actino-pnp
AdoCbl-variant Bacillaceae-1 Bacillus-plasmid Bacteroid-trp
Bacteroidales-1 Bacteroides-1 C4-a1b1 C4
Chlorobi-1 Chlorobi-RRM Chloroflexi-1 Clostridiales-1
Collinsella-1 Cyano-1 Cyano-2 Dictyoglomi-1
Downstream-peptide Flavo-1 Gut-1 JUMPstart
L17DE Lacto-rpoB Lacto-usp Lnt
Methylobacterium-1 Moco-II Ocean-V Pedo-repair
PhotoRC-I PhotoRC-II Polynucleobacter-1 Pseudomon-1
Pseudomon-Rho Pseudomon-groES Pyrobac-1 Rhizobiales-2
SAM-Chlorobi SAM-I-IV-variant SAM-II_long_loops SAM-SAH
STAXI Termite-flg Termite-leu TwoGGAY
asd atoC crcB EAR
flg-Rhizobiales flpD gabT glnA
gyrA hopC lactis-plasmid leu-phe_leader
livK manA mraW msiK
nuoG pan pfl potC
psaA psbNH radC rmf
rne-II sbcD sucA-II sucC
traJ-II wcaG whalefall-1 yjdF
ykkC-III

Alex wins the Benjamin Franklin award!

April 1, 2010

Our very own Alex Bateman has been awarded the prestigious Benjamin Franklin award! This is an annual award presented to someone in the community who has made significant contributions to promoting open access in the life sciences.

Nominations are made by at least two members of the community and then votes are collected by the good people at bioinformatics.org. Alex faced some stiff competition from many greats in the field yet still managed to win. He is the third Xfam associate who has won the award, joining Ewan Birney and Sean Eddy.

Naturally, all of the Xfam members are very happy with this result and are currently glowing in the reflected glory (or is that the result of the celebratory bubbly or the unseasonal weather).

Posted by: Rob and Paul.

Rfam, RNA Biology and Wikipedia in the news

February 20, 2009

Some of you may have noticed the recent attention that the unholy alliance between Rfam, RNA Biology and Wikipedia has been receiving recently. I thought it might be worthwhile posting a more detailed overview of how this happened, what we’re planning and dealing with the major criticisms.
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